PXD007935

PXD007935 is an original dataset announced via ProteomeXchange.

Title	Comparison of the MHC I immunopeptidome repertoire of B-cell lymphoblasts using two isolation methods
Description	Significant technological advances in both affinity chromatography and mass spectrometry have facilitated the identification of peptides associated with the major histocompatibility complex class I (MHC I) molecules, and enabled a greater understanding of the dynamic nature of the immunopeptidome of normal and neoplastic cells. While the isolation of MHC I-associated peptides (MIPs) typically used mild acid elution (MAE) or immunoprecipitation (IP), limited information currently exists regarding their respective analytical merits. Here, we present a comparison of these approaches for the isolation of two different B-cell lymphoblasts cell models, and report on the recovery, reproducibility, scalability and complementarity of identification from each method. Both approaches yielded reproducible datasets for peptide extracts obtained from 2 to 100 million cells, with 2016 to 5093 MIPs, respectively. The IP typically provides up to 6.4 fold increase in MIPs compared to the MAE. We extended the comprehensiveness of these immunopeptidome analyses using personalized genomic database of B-cell lymphoblasts, and discovered that 0.4 % of their respective MIP repertoire harbored non-synonymous single nucleotide variations (also known as minor histocompatibility antigens, MiHAs).
HostingRepository	PRIDE
AnnounceDate	2018-03-09
AnnouncementXML	Submission_2018-03-09_00:35:31.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD007935
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Courcelles Mathieu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Deamidated; Oxidation
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-10-10 05:23:01	ID requested
⏵ 1	2018-03-09 00:35:32	announced

Lanoix J, Durette C, Courcelles M, Cossette É, Comtois-Marotte S, Hardy MP, C, ô, t, é C, Perreault C, Thibault P, Comparison of the MHC I Immunopeptidome Repertoire of B-Cell Lymphoblasts Using Two Isolation Methods. Proteomics, 18(12):e1700251(2018) [pubmed]

curator keyword: Technical, Biological

submitter keyword: MHC I-associated peptides, MIPs, MAE, IP, Human, B-cell

Pierre Thibault
contact affiliation	Institute for Research in Immunology and Cancer, Department of Chemistry, Université de Montréal, Montréal, Québec, Canada H3T 1J4
contact email	pierre.thibault@umontreal.ca
lab head
Courcelles Mathieu
contact affiliation	IRIC
contact email	mathieu.courcelles@umontreal.ca
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/03/PXD007935

PRIDE project URI

• PRIDE
  1. PXD007935
     1. Label: PRIDE project
     2. Name: Comparison of the MHC I immunopeptidome repertoire of B-cell lymphoblasts using two isolation methods